rs4398173

Variant names:

• chr18-6941109-A-G
• rs4398173

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.437 in 152,136 control chromosomes in the GnomAD database, including 15,462 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.44 (15462 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.627
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66422 AN: 152016 Hom.: 15456 Cov.: 33

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.427

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.437 AC: 66450 AN: 152136 Hom.: 15462 Cov.: 33 AF XY: 0.430 AC XY: 31945 AN XY: 74362

African (AFR) AF: 0.350 AC: 14518 AN: 41502

American (AMR) AF: 0.324 AC: 4954 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1681 AN: 3472

East Asian (EAS) AF: 0.186 AC: 964 AN: 5174

South Asian (SAS) AF: 0.285 AC: 1377 AN: 4824

European-Finnish (FIN) AF: 0.552 AC: 5834 AN: 10562

Middle Eastern (MID) AF: 0.397 AC: 116 AN: 292

European-Non Finnish (NFE) AF: 0.525 AC: 35675 AN: 67994

Other (OTH) AF: 0.427 AC: 901 AN: 2110

Alfa AF: 0.484 Hom.: 58246

Bravo AF: 0.415

Asia WGS AF: 0.269 AC: 939 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.9
DANN	Benign	0.66
PhyloP100		0.63

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4398173; hg19: chr18-6941108;